Probing Steric and Hydrophobic Effects on Enzyme-Substrate Interactions by Protein Engineering

Abstract

Steric and hydrophobic effects on substrate specificity were probed by protein engineering of subtilisin. Subtilisin has broad peptidase specificity and contains a large hydrophobic substrate binding cleft. A conserved glycine (Gly 166 ), located at the bottom of the substrate binding cleft, was replaced by 12 nonionic amino acids by the cassette mutagenesis method. Mutant enzymes showed large changes in specificity toward substrates of increasing size and hydrophobicity. In general, the catalytic efficiency ( k cat /K m ) toward small hydrophobic substrates was increased (up to 16 times) by hydrophobic substitutions at position 166 in the binding cleft. Exceeding the optimal binding volume of the cleft (∼160 Å 3 ), by enlarging either the substrate side chain or the side chain at position 166, evoked precipitous drops in catalytic efficiency ( k cat /K m ) (up to 5000 times) as a result of steric hindrance.